NBCC Open Notebook Science Talk

Accelerating Discovery by Sharing: a case for Open Notebook Science Jean-Claude Bradley May 1, 2011 National Breast Cancer Coalition Annual Advocacy Conference Associate Professor of Chemistry Drexel University

Outline
Trends in sharing for drug discovery
ONS for malaria research
Crowdsourcing solubility with ONS
Leveraging the educational system to contribute new science
Open modeling and web services
Discovering connections
Moving forward: tools and practices

Industry is Sharing More

Opportunities for Competitive Collaboration

Some Initiatives Promoting More Openness in Drug Discovery

Motivation: Faster Science, Better Science

There are NO FACTS, only measurements embedded within assumptions Open Notebook Science maintains the integrity of data provenance by making assumptions explicit

TRUST PROOF

First record then abstract structure In order to be discoverable use Google friendly formats (simple HTML, no login) In order to be replicable use free hosted tools (Wikispaces, Google Spreadsheets) Strategy for an Open Notebook:

UsefulChem Project: Open Primary Research in Drug Design using Web2.0 tools Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.

Malaria Target: falcipain-2 involved in hemoglobin metabolism Dana.org

The Ugi Reaction

Outcome of Guha-Bradley-Rosenthal collaboration

References to papers, blog posts, lab notebook pages, raw data

The Ugi reaction: can we predict precipitation? Can we predict solubility in organic solvents?

Crowdsourcing Solubility Data

ONS Challenge Judges

ONS Challenge Award Winners

Solubilities collected in a Google Spreadsheet

Rajarshi Guha’s Live Web Query using Google Viz API

Data provenance: From Wikipedia to…

… the lab notebook and raw data

Interactive NMR spectra using JSpecView and JCAMP-DX

(Andy Lang, Tony Williams) Open Data JCAMP spectra for education (Andy Lang, Tony Williams, Robert Lancashire)

Raw Data As Images Splatter? Some liquid

YouTube for demonstrating experimental set-up

The importance of raw data availability Missed in a prior publication on solubility for this compound

Case study: Chemical Information Retrieval course at Drexel (Fall 2009/2010) Leveraging the educational system to contribute new science

The Chemical Information Validation Sheet 567 curated and referenced measurements from Fall 2010 Chemical Information Retrieval course

The Chemical Information Validation Explorer (Andrew Lang)

Discovering outliers for melting points (stdev/average)

Investigating the m.p. inconsistencies of EGCG

Investigating the m.p. inconsistencies of cyclohexanone

Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for melting points

Sigma-Aldrich, Acros and Wolfram Alpha apparently use the same sources for boiling points

Sigma-Aldrich, Acros and Wolfram Alpha apparently DO NOT use the same sources for flash points

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NBCC Open Notebook Science Talk

by Jean-Claude Bradley on May 01, 2011

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NBCC Open Notebook Science Talk — Presentation Transcript